Adam Novak
Senior Software Engineer at UC Santa Cruz Genomics Institute
Raleigh-Durham-Chapel Hill Area United States
Summary
🤩
Rockstar🎓
Top SchoolAdam Novak is a Senior Software Engineer with 13 years of experience building and scaling bioinformatics and distributed systems, currently at the UC Santa Cruz Genomics Institute. He combines deep C++ and Python expertise with hands-on DevOps work—implementing Kubernetes support for Toil and rewriting caching to behave correctly across filesystems. His research-driven engineering has produced published methods for mapping reads to graph-based pangenomes and substantial contributions to high-impact open-source projects like vg and vcflib that improve genome graph indexing and VCF structural-variant handling. Adam also brings systems-level savvy from work on encrypted networking (cjdns), automated workflow CI/CD, and Docker/Singularity integration. He mentors students, coordinates grant reporting, and has founded a small startup that explored Solidity-based procedural generation, reflecting both academic rigor and entrepreneurial curiosity.
13 years of coding experience
11 years of employment as a software developer
Bachelor of Science (BS), Computer Science and Biology, Bachelor of Science (BS), Computer Science and Biology at Harvey Mudd CollegeUniversity of California Santa CruzHigh School Diploma, High School Diploma at Illinois Mathematics and Science Academy
English
Github Skills (47)
algorithm10
unit-testing10
url-routing10
algorithms10
kubernetes10
graph-algorithms10
docker10
c-language10
python10
testing10
biopython10
sequence-alignment10
networking10
dockers10
data-structure10
Programming languages (34)
Github contributions (5)
vgteam/vg
Jul 2015 - Jan 2023
tools for working with genome variation graphs
Role in this project:
Back-end Developer & Infrastructure Engineer
Back-end Developer & Infrastructure EngineerContributions:46 releases, 69 reviews, 5118 commits in 7 years 8 months
Contributions summary:Adam's commits focused on building out and refining the autoindex functionality, specifically related to the construction and augmentation of Genome Variation Graphs (GVG) and GBWT indexes. They made changes to incorporate embedded paths from graphs, refined the handling of various path metadata, and worked on improving the efficiency of the index building process with the use of chaining. Furthermore, the user appears to have worked on the underlying infrastructure that powers this functionality.
genomegenome-graphdnagenomicsbioinformatics
DataBiosphere/toil
Sep 2015 - Jan 2023
A WDL, CWL and Python API supporting easy-to-use workflow engine. It is scalable, efficient and cross-platform (Linux/macOS).
Role in this project:DevOps Engineer
DevOps EngineerContributions:5 releases, 905 reviews, 1071 commits in 7 years 6 months
Contributions summary:Adam's commits primarily focus on the configuration and maintenance of infrastructure and deployment processes for the Toil project. The user added and updated scripts, and automation, for building and deploying the project within a Kubernetes environment. The commits demonstrate the user's expertise in configuring and building docker images and ensuring correct file permissions for a production environment. Furthermore, the user added testing for the automated building, loading, and uploading of files to Amazon S3, while also applying code reviews and fixing typing and syntax mistakes to increase code quality.
linuxmacospythonwdlworkflow-engine
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